From stress to acclimation : a systems biology look on the life of Saccharomyces cerevisiae in industrial bioreactors

Abstract

Carbon limitation is a fundamental feeding strategy in commercial fermentations guaranteeing efficient substrate-to-product conversion. However, industrial reaction volumes often prevent a microbe from performing optimally. One common source of interference is insufficient mixing resulting in the formation of concentration gradients. For instance, faster microbial consumption versus convective supply depletes the highly diluted limiting substrate locally. The industrial workhorse Saccharomyces cerevisiae (S. cerevisiae) naturally possesses adaptive mechanisms to cope with substrate depletion. Whether triggered response mechanisms benefit strain performance is doubtful, given that enough substrate is present in an industrial carbonlimited process on average. On the contrary, unnecessary or futile adaptation mechanisms often cause unexpected microbial behavior on large scales. Exploring and elucidating this behavior is the focal point of this thesis. The presented case study employs a stimulus-response approach mimicking a baker’s yeast fermentation snapshot featuring non-ideal starvation zones. In brief, glucose-limited chemostats with two-minute intervals of stopped feeding induce transitions between limitation and starvation. Metabolomic and transcriptomic measurements enable a systems biology analysis of either non-adapted or stimulus-adapted yeasts. One part of this study investigates the haploid laboratory strain CEN.PK113-7D under aerobic conditions. Another part reports gene expression dynamics of the diploid industrial strain Ethanol RedTM under anaerobic conditions. Both strains display robust growth under the tested conditions at the cost of tactic and strategic investments. The laboratory yeast responds to a 110 μmol·L-1 glucose gradient with a modified energy and redox homeostasis. Non-adapted cells perceive this stimulus as a threat, as evidenced by a futile triggering of the environmental stress response causing transient growth rate reduction and increased maintenance demand. Complete adaptation evokes a distinct ‘bioreactor phenotype’ characterized by increased growth capacities and repressed stress response. Results obtained with Ethanol RedTM confirm this stress defense-growth trade-off to be a conserved implication in bioprocesses with fluctuating carbon supply. Altogether, the findings presented in this thesis contribute to a fundamental understanding of how S. cerevisiae operates in heterogeneous commercial-scale fermentations. Finally, the gained knowledge reveals optimization targets for both strain engineering and bioprocess development.